A common endpoint for biomarker discovery experiments is a list of putative marker proteins. A reasonable next step is to then perform targeted quantitative measurements of these proteins in an expanded patient population to assess their validity as markers. In one approach, selective reaction monitoring (SRM) based targeted discovery is used to filter a list of putative biomarkers down to a more targeted one. Starting with a peptide of interest, candidate fragment ions are chosen to set m/z values in the Q1/Q3 cells of a triple quadrupole mass spectrometer. As the sample flows through the liquid chromatography (LC) column, Q1/Q3 cells periodically measure signals for the m/z settings.
Unfortunately, in a complex background like plasma, various analytes can yield signals that approximate the peptide of interest, thereby leading to false positives. To quantify correctly the peptide of interest it is critical to be able to discriminate between these analytes, and identify the correct retention time of the peptide.
Accordingly, there exists a need for a method that overcomes at least some of the above-mentioned limitations.